Sonic hedgehog (Shh) is required for axon guidance of commissural neurons during spinal cord development, which involves reorganization of the actin cytoskeleton. Even if it is known that this process is regulated by small Rho GTPases, an effect of Shh on these proteins has not been clearly demonstrated. In this study, we show that Shh activates the small GTPases Rac1 and Cdc42. This activation occurs rapidly, which is compatible with the guidance effects of Shh on commissural neurons. In parallel, we characterized the Shh-dependent activation of Boc, which is a Shh receptor required for commissural axon guidance. Taken together, these results help refine our understanding of the signal transduction mediated by Shh during axon guidance of commissural neurons.